findhotpixels(1) General Commands Manual findhotpixels(1)
NAME
findhotpixels - find pixels to exclude from X-ray analysis in SerialEM
SYNOPSIS
findhotpixels [options] input_image output_model
DESCRIPTION
Findhotpixels will analyze a set of CCD camera dark reference images to
identify relatively hot pixels in the CCD chip and will output a list
of the pixels in a format suitable for placing in the property file for
SerialEM. Automatic removal of X-rays from dark references can then be
activated in SerialEM, and it will then be able to avoid identifying a
hot pixel as an X-ray. It is recommended that three long-exposure
(e.g., 3 sec) dark reference images be used for this analysis.
The program works by finding pixels that deviation from the image mean
by a specified threshold. The lower the threshold, the more pixels it
will find. You may need to run the program several times to find a
threshold that gives a reasonable number of hot pixels (under 100). A
threshold on the order of 0.2% of the dynamic range of the camera
should be appropriate.
Hot columns are excluded from the analysis. With 4-port readout cam-
eras from Gatan, it is important to exclude a fairly large number of
bright columns near the edges; otherwise you will need to set the
threshold higher than the optimal level for finding the hot pixels in
the rest of the camera. The program could be smarter about this and
use a deviation from a local mean, but there is no point in doing so
under SerialEM uses a local criterion as well.
The program outputs a list of the hot pixels coordinates and their val-
ues above the image mean. At the end is a set of HotPixels and Hot-
Columns entries suitable for pasting into the SerialEM properties file.
OPTIONS
The program can be run either interactively or with command line argu-
ments processed by the PIP interface (see the man page for pip).
With command line arguments, the options are:
-input OR -InputFileFilename
Name of input image file with dark reference images. If this
option is not entered, the first non-option argument is used
-output OR -OutputFileFilename
Name of output model file with a point at every hot pixel. If
this option is not entered, the second non-option argument is
used.
-columns OR -HotColumnsListofintegerranges
List of hot columns to exclude (numbered from 0). Ranges may be
entered.
-threshold OR -ThresholdDifferenceFloatingpoint
Threshold difference from mean value for seeking hot pixels
-help OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
INTERACTIVEINPUTS
If no command line arguments are entered, input is requested interac-
tively as follows:
Name of input image file with dark reference images
Name of output model file with a point at every hot pixel
List of hot columns to exclude (numbered from 0)
Threshold difference from mean value for seeking hot pixels
HISTORY
Written by David Mastronarde in 2003. Added to IMOD, 10/17/06.
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.10.12 findhotpixels(1)